why taxonomy? how to determine & classify a species ... · pdf filehow to determine &...
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Why Taxonomy?
How to determine & classify a species
Domains versus Kingdoms
Phylogeny and evolution
Taxonomy
Why Taxonomy?
• Classification – Arrangement in groups or taxa
(taxon = group)
• Nomenclature – Assigning names to taxa
• Identification – Determination of taxon to which an
isolate belongs
(Most practical part of taxonomy)
Making sense of Nature
Classification
Comparison of species based on:
• Natural – anatomical characteristics• Phenetic – phenotypic characteristics• Genotypic – genetic characteristics• Phylogenetic – evolutionary links
Polyphasic Taxonomy
• used to determine the genus and species of a newly discovered procaryote
• incorporates information from genetic, phenotypic and phylogenetic analysis
genus – well defined group of one or more species that is clearly separate from other genera
Defining procaryotic species & strains
• Definition species:– collection of strains that share many stable properties and
differ significantly from other groups of strains
• Alternative definition:– collection of organisms that share the same sequences in
their core housekeeping genes
• Strain:- descended from a single, pure microbial culture- Type strain: usually one of first strains of a species studied
Numerical Taxonomy• To create phenetic classification systems• multistep process
– code information about properties of organisms• e.g., 1 = has trait; 0 = doesn’t have trait
– use computer to compare organisms on ≥ 50 characters
– determine association coefficient– construct similarity matrix– identify phenons and construct dendograms
Association coefficients
• Simple matching coefficient (SSM)
• Jaccard coefficient– ignores characters
that both lack
Figure 19.6
similaritymatrix
rearranged andjoined to show clusters
• dendogram – treelike diagram used to display results
dendogram
• phenon – group of organisms with great similarity– phenons with ≥80% similarity = bacterial species
Techniques for Determining Microbial Taxonomy and Phylogeny
• Classical CharacteristicsMorphological
EcologicalPhysiologicalBiochemical
Genetic
Ecological Characteristics
life-cycle patternssymbiotic relationshipsability to cause disease
habitat preferencesgrowth requirements
Molecular Characteristics
Comparison of proteinsNucleic acid base composition
Nucleic acid hybridizationNucleic acid sequencing
Nucleic acid base composition
G + C content
- Mol% G + C = (G + C/G + C + A + T)100
- Often determined from melting temperature (Tm)
- Variation within a genus usually < 10%
Figure 19.8 DNA melting curve.
as temperature slowlyincreases, hydrogen bondsbreak, and strandsbegin to separate
DNA issinglestranded
Figure 19.9
Nucleic acid hybridization
• measure of sequence homology• common procedure:
– bind nonradioactive DNAto nitrocellulose filter
– incubate filter with radioactivesingle-stranded DNA
– measure amount of radioactiveDNA attached to filter
Nucleic acid sequencing
• most powerful and direct method for comparing genomes
• sequences of 16S & 18S rRNA (SSU rRNAs) are used most often in phylogenetic studies
• complete chromosomes can now be sequenced and compared(BIOINFORMATICS !)
Genetic Analysis
• study of chromosomal gene exchange by transformation and conjugation– these processes rarely cross genera
• plasmids can help to solve confusion in the analysis of phenotypic traits
The Major Divisions of Life
• Currently held: 3 domains of life:–Bacteria–Archaea–Eucarya
• Scientists do not all agree aboutthis way of the “Tree of Life”
Comparative Analysis of 16S rRNA sequences
• Oligonucleotide signature sequences– short conserved sequences specific for a phylogenetically
defined group of organisms
• Organisms relatedness = association coefficient (Sab)
– the higher the Sab value, the more closely related the organisms